#change pop to AFA
 #perl perl_gen_table.pl

mv filetered_r2_0_03.out AFA_filetered_r2_0_03.out
mv filetered_r2_0_08.out AFA_filetered_r2_0_08.out
#create table
perl perl_generate_table_count_snps.pl unfiletered.out AFA_filetered_r2_0_03.out AFA_filetered_r2_0_08.out > table_AFA

perl perl_filter_chn_maf.pl 9 AFA_MAF_0.02 0.02
perl perl_filter_chn_maf.pl 9 AFA_MAF_0.05 0.05
perl perl_chn_maf_filter.pl AFA_MAF_0.02 unfiletered.out unfiletered_AFA_MAF_0.02.out
perl perl_chn_maf_filter.pl AFA_MAF_0.05 unfiletered.out unfiletered_AFA_MAF_0.05.out
perl perl_chn_maf_filter.pl AFA_MAF_0.02 AFA_filetered_r2_0_03.out AFA_filetered_r2_0_03_AFA_MAF_0.02.out
perl perl_chn_maf_filter.pl AFA_MAF_0.02 AFA_filetered_r2_0_08.out AFA_filetered_r2_0_08_AFA_MAF_0.02.out
perl perl_chn_maf_filter.pl AFA_MAF_0.05 AFA_filetered_r2_0_03.out AFA_filetered_r2_0_03_AFA_MAF_0.05.out
perl perl_chn_maf_filter.pl AFA_MAF_0.05 AFA_filetered_r2_0_08.out AFA_filetered_r2_0_08_AFA_MAF_0.05.out

perl perl_generate_table_count_snps.pl unfiletered_AFA_MAF_0.02.out AFA_filetered_r2_0_03_AFA_MAF_0.02.out AFA_filetered_r2_0_08_AFA_MAF_0.02.out > table_AFA_MAF_0.02.out
perl perl_generate_table_count_snps.pl unfiletered_AFA_MAF_0.05.out AFA_filetered_r2_0_03_AFA_MAF_0.05.out AFA_filetered_r2_0_08_AFA_MAF_0.05.out > table_AFA_MAF_0.05.out
